The Blue Brain Project news
In a front-cover paper published in Cerebral Cortex, EPFL’s Blue Brain Project, a Swiss Brain Research Initiative, explains how the shapes of neurons can be classified using mathematical methods from the field of algebraic topology.
The Blue Brain Project is delighted to announce that it will be hosting in May this year, the second Neuromodulation of Neural Microcircuits NM² Conference.
Blue Brain’s Cristina Colangelo wins Best Flash Talk at the first Swiss Early-Career Researchers Symposium
The first digital 3D atlas of every cell in the mouse brain provides neuroscientists with previously unavailable information on major cell types, numbers and positions in all 737 brain regions – which will potentially accelerate progress in brain science massively. Released by EPFL’s Blue Brain Project and published in Frontiers in Neuroinformatics, the Blue Brain Cell Atlas integrates data from thousands of whole brain tissue stains into a comprehensive, interactive and dynamic online resource that can continuously be updated with new findings.
The Blue Brain Project will be part of the Nomads Foundation exhibition ‘Futur des métiers’ at the Cité des Métiers taking place in the Palexpo Exhibition Centre, Geneva, Switzerland this November.
The EPFL Blue Brain Project recently welcomed a delegation of primary and secondary school heads and Neurology students from Slovenia to the Campus Biotech.
The Blue Brain Project is delighted to be taking part in ‘Planète Santé Live’ at the Palexpo Exhibition Centre, Geneva, Switzerland. October 4-7, 2018.
Originally, one of Blue Brain’s first domain specific interactive visualization tools, the latest version of RTNeuron provides a scalable real-time rendering tool for the visualization of detailed neuronal simulations based on cable models. This allows the visualization of neurons, synapses and playback of simulation data as well as other basic geometrical objects.
Blue Brain was delighted to welcome the New York Times Student Journeys groups for a visit to the Project. The New York Times Student Journeys offers educational travel programs for high school students and Blue Brain is part of the itinerary during their three-week visit to Switzerland.
EPFL Blue Brain Project deploys its next supercomputer – Blue Brain 5
Hewlett Packard Enterprise (HPE) today announced that the Ecole Polytechnique Fédérale de Lausanne’s (EPFL) Blue Brain Project, a Swiss brain research initiative, selected HPE to build a next-generation supercomputer for modeling and simulation of the mammalian brain. The new supercomputer, called ‘Blue Brain 5’, will be dedicated to simulation neuroscience, in particular simulation-based research, analysis and visualization, to advance the understanding of the brain.
Click here to read the HPE announcement.
Blue Brain is delighted to be a supporting partner as the SIB Swiss Institute of Bioinformatics celebrate its 20-year anniversary.
Frontiers hosted its second Data Services Workshop in Brussels on April 24 with this year’s workshop focusing on the application of open research data to support sustainable health initiatives. Drawing lessons from recent successes in the use of big data and artificial intelligence in data-intensive health research, it aimed to discuss policy challenges and actions necessary in Europe to unleash the full potential of open research data in health for the benefit of society.
Blue Brain’s Operations Director Adriana Salvatore presented the Blue Brain Project to a group of 100 MBA students from the IMD Business School with a specific focus on the operational side of the project.
Knowledge sharing is an important driving force behind scientific progress. In an open-science approach, EPFL’s Blue Brain Project has created and open sourced Blue Brain Nexus that allows the building of data integration platforms. Blue Brain Nexus enables data-driven science through searching, integrating and tracking large-scale data and models.
A team of scientists led by Eilif Muller of the Blue Brain Project, have had their INCITE grant renewed for 2018 to provide a further 160 million core hours at the Argonne National Laboratory. INCITE supports computationally intensive, large-scale research projects with large amounts of dedicated time on supercomputers at DOE’s Leadership Computing Facilities. In 2017, INCITE awarded the Blue Brain with 100 million core hours to simulate biophysical synaptic plasticity in reconstructions of the neocortical microcircuit to discover their synergistic functional principles.
During our lifetimes, our brains undergo continuous changes as a consequence of our experiences. Synaptic plasticity—the biological process by which brain activity leads to changes in synaptic connections, is thought to be central to learning and memory. However, little is known about how this process shapes biological neural networks.
With this renewed grant, the team that also includes scientists from the École polytechnique fédérale de Lausanne and The Hebrew University of Jerusalem will continue to focus on advancing our understanding of these fundamental mechanisms of the brain’s neocortex. The team is carrying out large-scale simulations of recently uncovered biophysical principles underlying synaptic plasticity in reconstructions of a neocortical microcircuit (Markram et al., 2015; 10.1016/j.cell.2015.09.029) consisting of around 200,000 neurons and 260 million synapses. The aim is to shed light on the synergistic functional principles that shape plasticity in realistic cortical circuits.
The team is also using DOE supercomputers to characterize: (1) the role of NMDA receptor spikes in plasticity induction; (2) the dynamics of neuronal assembly formation and maintenance; and (3) the computational impact of synaptic plasticity in common signal processing tasks. In addition to improving our understanding of the brain, this research could help inform the development of enhanced deep learning methods, as well as new learning paradigms for neuromorphic hardware.
Click here to read the INCITE announcement.
Register for the MOOC: Simulation Neuroscience – reconstruction of a single neuron
A unique, massive open online course taught by a multi-disciplinary team of world-renowned scientists
Simulation Neuroscience is an emerging approach to integrate the knowledge dispersed throughout the field of neuroscience.
The aim is to build a unified empirical picture of the brain, to study the biological mechanisms of brain function, behaviour and disease. This is achieved by integrating diverse data sources across the various scales of experimental neuroscience, from molecular to clinical, into computer simulations.
In this first course, you will gain the knowledge and skills needed to create simulations of biological neurons and synapses.
This course is part of a series of three courses, where you will learn to use state-of-the-art modeling tools of the Human Brain Project Brain Simulation Platform to simulate neurons, build neural networks, and perform your own simulation experiments. We invite you to join us and share in our passion to reconstruct, simulate and understand the brain!
What you’ll learn
- Discuss the different types of data for simulation neuroscience
- How to collect, annotate and register different types of neuroscience data
- Describe the simulation neuroscience strategies
- Categorize different classification features of neurons
- List different characteristics of synapses and behavioural aspects
- Model a neuron with all its parts (soma, dendrites, axon, synaps) and its behavior
- Use experimental data on neuronal activity to constrain a model
Meet the instructors:
Henry Markram – Professor EPFL, Founder and Director of the Blue Brain Project
Idan Segev – David & Inez Myers Professor in Computational Neuroscience at Hebrew University Jerusalem, and Adjunct Professor EPFL.
Sean Hill – Adjunct Professor EPFL, Blue Brain Project, Director of the Krembil Centre of Neuroinformatics at the Centre of Addiction and Mental Health in Toronto, Canada
Dr. Felix Schürmann – Adjunct Professor EPFL, Director Blue Brain Project
Dr. Eilif Muller – Section Manager, Cells & Circuits, Simulation Neuroscience, Blue Brain Project
Dr. Srikanth Ramaswamy – Senior Scientist, Cells & Circuits, Simulation Neuroscience, Blue Brain Project
Werner Van Geit – Systems Specialist, Neuroscientific Software Engineering, Computing, Blue Brain Project
Samuel Kerrien – Section Manager, Neuroinformatics Software Engineering, Computing, Blue Brain Project
Lida Kanari – PhD Student, Molecular Systems, Simulation Neuroscience, Blue Brain Project
The course is targeted at senior bachelor, master or PhD students in science or engineering fields looking for an introduction to Simulation Neuroscience.
It is a six-week course, with an estimated course load of 5-7 hours per week.
- Knowledge of ordinary differential equations, and their numerical solution
- Knowledge of programming in one of Python (preferred), C/C++, Java, MATLAB, R
Successful Neuromodulation of Neural Microcircuits NM² Conference prompts future collaborations
At the end of September, the Blue Brain Project concluded a stimulating, interactive and highly collaborative Neuromodulation of Neural Microcircuits NM² Conference. A global line-up of renowned speakers and more than one hundred attendees from across the different Neuromodulation communities ensured a cross-pollination of experience and expertise throughout the three-day Conference.
Neuromodulators – the master switches – dynamically reconfigure neural microcircuits and shape brain states by controlling the function of neurons and glia, dendrites, and synapses. Recently, the Blue Brain Project discovered that neocortical microcircuit activity shifts from synchronous to asynchronous network states that is tightly controlled by neuronal and synaptic physiology. This effect is strikingly similar to the function of neuromodulators, which control neurons and synapses to sculpt the emergence of brain states.
Therefore, understanding the mechanisms by which neuromodulators operate is not only fundamental to Blue Brain’s pioneering work in simulating brain function and dysfunction, but also the global neuroscience community. Over the three days of the Conference, 34 leading experts in this field presented their current research and enthusiastically participated in panel discussions, as both speakers and participants took part in shaping the future course of neuromodulatory research. Srikanth Ramaswamy, NM² Conference Host said “This meeting is unique in that it focuses on the mechanisms by which diverse neuromodulators could give rise to similar behavioral states by differentially controlling neuronal and synaptic activity.”
With a strategic focus on the neuromodulation of microcircuits, the Conference provided a platform to identify common principles by which different neuromodulators regulate the activity of neurons and glia, dendrites, and synapses. Speaker and day three Chair Randy Bruno said “Biologists have been listening to the raucous activity of neural circuits for a century. Only recently have we begun to appreciate how neuromodulation quietly orchestrates it all”.
The successful NM2 Conference has not only provided a springboard to shape a follow-up event in 2019, but has also laid the foundation towards an international consortium to drive collaborative research in neuromodulation.
A Topological Representation of Branching Neuronal Morphologies
In a paper published in the journal Neuroinformatics, a team of scientists led by the Blue Brain Project, in collaboration with the Laboratory for Topology and Neuroscience, explain how the invention of the Topological Morphology Descriptor (TMD), provides a method for encoding the spatial structure of any tree as a “barcode”, a unique topological signature.
Many biological systems consist of branching structures that exhibit a wide variety of shapes. Understanding of their systematic roles is hampered from the start by the lack of a fundamental means of standardizing the description of complex branching patterns, such as those of neuronal trees.
As opposed to traditional morphometrics, the TMD couples the topology of the branches with their spatial extents by tracking their topological evolution in 3-dimensional space. The team prove that neuronal trees, as well as stochastically generated trees, can be accurately categorized based on their TMD profiles.
The TMD retains sufficient global and local information to create an unbiased benchmark test for their categorization and is able to quantify and characterize the structural differences between distinct morphological groups. The use of this mathematically rigorous method will advance our understanding of the anatomy and diversity of branching morphologies.
Click here to read the paper.
Comprehensive Morpho-Electrotonic Analysis Shows two Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex
The group of Idan Segev of the Hebrew University of Jerusalem and Christiaan P.J. de Kock of the Vrije Universiteit, Amsterdam, in collaboration with the Molecular Systems Section in the Simulation Neuroscience Division of the Blue Brain Project, employed feature-based statistical methods, on a rare data set of 60 3D reconstructed pyramidal neurons from L2 and L3 in the human temporal cortex (HL2/L3 PCs) removed after brain surgery.
Of these cells, 25 neurons were also characterized physiologically. Thirty-two morphological features were analyzed, 18 of which showed a significant gradual increase with depth from the pia (e.g., dendritic length and soma radius). The other features showed weak or no correlation with depth (e.g., dendritic diameter).
The basal dendritic terminals in HL2/L3 PCs are particularly elongated, enabling multiple nonlinear processing units in these dendrites. Unlike the morphological features, the active biophysical features (e.g., spike shapes and rates) and passive/cable features (e.g., somatic input resistance, membrane time constant, and dendritic cable length) appear to be depth-independent.
A novel topological descriptor for apical dendrites yielded two distinct classes, termed hereby as “slim-tufted” and “profuse-tufted” HL2/L3 PCs. The two classes also differ in their electrical properties, as the “profuse-tufted” cells tend to fire at higher rates. Therefore, two distinct morpho-electrotonic classes of HL2/L3 Pcs were identified for the first time.
Click here to read the paper published in Cerebral Cortex.
The Blue Brain Project launches three-day conference to kick-start neuromodulation research – NM2
- NM² Conference to address understanding the mechanisms by which neuromodulators operate which is both fundamental to Blue Brain’s pioneering work in simulating brain function and dysfunction, and for the global neuroscience community
- Leading experts from around the world and EPFL to present and take part in panel discussions across the three days
- NM2² Conference to provide a unique platform for students and junior researchers to interact with leaders in the field to collectively take part in shaping the future course of neuromodulatory research
The Blue Brain Project is delighted to announce that it will be hosting a three-day conference – Neuromodulation of Neural Microcircuits NM² from September 18th to 20th, 2017.
Neuromodulators – the master switches – dynamically reconfigure neural microcircuits and shape brain states by controlling the function of neurons and glia, dendrites, and synapses. Recently, the Blue Brain Project discovered that neocortical microcircuit activity shifts from synchronous to asynchronous network states that is tightly controlled by neuronal and synaptic physiology. This effect is strikingly similar to the function of neuromodulators, which control neurons and synapses to sculpt the emergence of brain states. Therefore, understanding the mechanisms by which neuromodulators operate is not only fundamental to Blue Brain’s pioneering work in simulating brain function and dysfunction, but also the global neuroscience community.
The Conference will bring together world-leading experts to:
- Identify the state-of-the-art mechanisms of the neuromodulation of neural microcircuits
- Illuminate various strategies enabling the measurement of neuromodulatory states in brain health and disease
- Integrate knowledge to build a unifying view of the neuromodulation of different brain region
- Inform and attract new talent to drive forward neuromodulation research
- Inspire future directions that will transform our understanding of the neuromodulation of brain function and dysfunction and therapeutic intervention
- The NM² Conference will also provide a unique platform for students and junior researchers to interact with leaders in the field to collectively take part in shaping the future course of neuromodulatory research. Students and postdocs attending the event are invited to submit abstracts during registration to present a poster at the Conference.
Conference Host and Blue Brain Senior Scientist, Srikanth Ramaswamy is greatly looking forward to the event; “The NM² Conference will bring together researchers to bridge a variety of disciplines using state-of-the-art techniques in different brain regions towards the common goal of understanding the mechanisms and principles of neuromodulation.”
Founder and Director of the Blue Brain Project, Prof. Henry Markram commented; “The NM² Conference is designed to foster cross-disciplinary collaborations that will pave the way to enable the next breakthroughs in understanding the neuromodulatory control of brain states. We look forward to welcoming all conference speakers and participants.”
The first two days of the Conference 18-19 September, are being held at the SwissTech Convention Center on the EPFL Campus in Lausanne, before the Conference moves on 20 September to the Headquarters of Blue Brain at the Campus Biotech in Geneva.
Comprehensive Morpho-Electrotonic Analysis Shows two Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex.
In a paper published today, a team of scientists led by the Blue Brain Project have used a sophisticated type of mathematics in a way that it has never been used before in neuroscience.The team have uncovered a universe of multi-dimensional geometrical structures and spaces within the networks of the brain.
This research, published in Frontiers in Computational Neuroscience, has significant implications for our understanding of the brain.
Uncovering structural regularities and architectural topologies of cortical circuitry is vital for understanding neural computations.
In a paper published in Nature Neuroscience, the group of Idan Segev of the Hebrew University of Jerusalem in collaboration with the Cells & Circuits team in the Simulation Neuroscience Division of the Blue Brain, and Tel Aviv University identified a rich cell-type-specific network topology in neocortical microcircuitry. The systematic approach presented in the paper has enabled interpretation of microconnectomics ‘big data’, and provided several experimentally testable predictions.
here to read the paper.
Blue Brain wins major award of supercomputing time from DOE
A Blue Brain team, led by Eilif Muller, has won a major award of supercomputing time, from the DOE’s prestigious Incite Leadership Computing Program. The award gives the team an unprecedented opportunity to simulate synaptic plasticity—the process through which brain activity shapes synaptic connections. The study – which will build on Blue Brain’s recently published reconstruction of neural microcircuitry – it will focus on the impact of plasticity on the detailed organization and functioning of neural networks. The results will provide insights, not just to neuroscientists but also to technologists, seeking to implement brain-like learning mechanisms in software and hardware. To see the Incite Announcement click here.
On, the US-based Allen Institute released a set of 40 computer models of neurons from the mouse visual cortex, created using tools developed by the Blue Brain Project. Using Blue Brain technology, the researchers were able to reproduce the physiology and electrical activity of the neurons with an extremely high level of detail. For further details click here.
Blue Brain Project releases Open Source Software providing model parameter optimization for neuroscientists
The Allen Brain Institute recently used Blue Brain modelling and optimization tools to model neurons from mouse visual cortex (see news below). Now other neuroscientists can use Blue Brain tools to optimize their own models. The Blue Brain Project has just released the BlueBrain Python Optimization Library (BluePyOpt) – an extensible open source framework for data-driven model parameter optimisation that wraps and standardises several existing open-source tools. The library includes methods for setting up small- and large-scale optimizations on a broad range of compute platforms – from laptops to large cloud-based compute infrastructures. The code can be downloaded here. A preprint describing the library is available here.
The Blue Brain Project has announced the opening of the Neocortical Microcircuit Collaboration Portal (NMC-Portal). The NMC portal allows researchers with access to the Internet, to access the experimental data used in the reconstruction, to download cellular and synaptic models, and to analyze the predicted properties of the microcircuit It also provides data supporting comparison of the anatomy and physiology of the reconstructed microcircuit against results in the literature. The aim is to catalyse community efforts to understand the cellular and synaptic organization of neocortical microcircuitry (ion channels and their densities, neuron types and their distributions across layers, connectivity between neurons, synapse types, synaptic properties etc.).. Future periodic releases will incorporate results from these efforts. To read more about the portal click here. To access the portal itself click here.
A paper published today describes a mathematical algorithm that predicts the location of nearly 40 million synapses formed between the neurons in a small block of brain tissue about 100’000 times larger than has ever been analyzed with electron microscopy. The algorithm uses millions of times less experimental data than would normally be needed using purely experimental methods. The algorithm was developed as part of the Blue Brain Project’s mission to digitally reconstruct the biological detail of the brain and is a companion paper to the team’s paper on the Reconstruction and Simulation of Neocortical Microcircuitry.
The Blue Brain Project, the simulation core of the Human Brain Project, has completed a first draft computer reconstruction of a piece of the neocortex. The electrical behavior of the virtual brain tissue was simulated on supercomputers and found to match the behavior observed in a number of experiments on the brain. Further simulations revealed novel insights into the functioning of the neocortex. This first step towards the digital reconstruction and simulation of the brain is published in Cell.
The Blue Brain Project visualization team has recently published an article on the modeling and simulation of brain imaging with light sheet fluorescence microscope (LSFM) on a physically plausible basis. This model reflects the light propagation in the optical setup of the LSFM using Monte Carlo rendering taking into account the physics of geometric optics. It can accurately render synthetic optical sections that are comparable to realistic ones produced by the LSFM. This in silico LSFM will be potentially employed for validating the reconstructed tissue models from microscopic imaging stacks.
The Blue Brain Project’s High Performance Computing Team (HPC) has been selected by the Argonne Leadership Computing Facility (ALCF) to participate in the 2-year Theta Early Science Program. This program will target the porting and optimization at large scale of our CoreNeuron scientific application on ALCF next leadership-class supercomputer prototype, Theta. This opportunity will allow the HPC team developers to collaborate with Intel, Cray and ALCF HPC specialists to drive the development of CoreNeuron to support 4 challenging scientific use cases: (a) The analysis of the electrical activity of the mouse brain Somatosensory Cortex, (b) The study of Synaptic Plasticity phenomenon in a mouse brain, (c) The building and simulations of a full mouse brain model and (d) The study of the activity and plasticity of a mouse brain model when embedded into a simulated body interacting within its environment.
NEST User Workshop, 20-22 April 2015 in Geneva and Connectomics School, 9-16 May 2015, Florence.
EPFL and the Chinese Academy of Sciences will collaborate on Neuroinformatics platforms, Data and Knowledge integration, algorithms for Brain Reconstruction and Brain Atlas platforms.
Neurorobotics engineers from the Human Brain Project (HBP) have recently taken the first steps towards building a “virtual mouse” by placing a simplified computer model of the mouse brain into a virtual mouse body.
Sean Hill explains how computer models of individual neurons are being assembled into neural circuits that produce electrical signals akin to brain waves.
Grâce a lui, les chercheurs de l’EPFL pourront reproduire, en trois dimensions, les 70 millions de neurones d’un cerveau de souris >>.
For almost a century, scientists have been studying brain waves to learn about mental health and the way we think >>.
The organizers of the BMI Research Day are happy to announce the program of the 2nd BMI Research Day 2014. The event takes place on June 11th and will start at 11:50 in EPFL (SV1717A / SV Lobby).
For all media enquiries, please contact Kate Mullins – Communications Manager